On its way to ravaging cities and towns in north Queensland, severe tropical cyclone Yasi will almost certainly have left a swath of destruction on the Great Barrier Reef off Townsville.

Early last month, as floods struck southern Queensland, I accompanied a team of divers from the Australian Institute of Marine Science on an expedition to a 300-mile part of the reef – a fifth of the 1,400-mile-long World Heritage Area.

The researchers dived 13 reefs – from Myrmidon, which is 75 miles out to sea, to areas around the inshore Palm Island group, just off the mainland. Much of what we saw was spectacular and showed the reef recovering from a decade of devastation caused by coral bleaching and crown-of-thorns starfish, both of which have been responsible for large areas of coral mortality.

It may be weeks or months before scientists can fully survey and assess the damage from cyclone Yasi but, based on the effect of previous large cyclones, they will not be optimistic. Tropical cyclones generate huge waves, which pulverise coral reefs into rubble.

In March 2009, category four tropical cyclone Hamish travelled in an unusual path from north to south, tracking parallel to the coast and not making landfall. It is estimated to have affected a quarter of the Great Barrier Reef.

A year later I was able to dive in one of the areas hit by cyclone Hamish, also with scientists from the Australian Institute of Marine Science. Much of what we saw at the Swains, at the southern end of the Great Barrier Reef, was denuded of life. Numerous coral bommies, many the size of big cars, had been lifted up on to the reef flat by the force of the storm. It can take years, or even decades, for such a coral ecosystem to recover fully.

Scientists fear that as climate change tightens its grip devastating storms such as cyclones Yasi and Hamish will become more frequent and intense. However, it is not just the direct impacts of these storms that can damage the reef.

In the wake of the Queensland flooding, a coral ecologist at the Australian Institute of Marine Science, Dr Katharina Fabricius, warned that floodwaters carrying high nutrient loads from agricultural and urban catchments could lead to outbreaks of crown-of-thorns starfish. The starfish feed on coral, quickly denuding entire reefs.

Last year Fabricius and her colleagues published new evidence that nutrients in floodwaters provide food to the starfish larvae, increasing their survivability.

These are nervous days for the marine biologists who study the Great Barrier Reef and the authorities responsible for its good health.

James Woodford is the author of The Great Barrier Reef (Pan Macmillan)